Geni's team asked previously for me to demonstrate when this happens, and it has happened a few times in the past couple of months: I'm given a line that isn't the closest, shown a cousin or uncle relationship when the individual is a great grandparent. Here's the latest:
I've established that Simon de Montfort (https://www.geni.com/people/Simon-de-Montfort-6th-Earl-of-Leicester/6000000002267701247) is twice my great grandfather via Richard FitzSimon de Montfort and Eleanor de Montfort, Princess of Wales and Lady of Snowdon but instead Geni has given me this (2nd cousin):
and this (great uncle by marriage):
Granted it's possible that there have been changes to these lines, but it's unlikely. If it were only one line I would probably assume that that is what happened.
Thanks...